Ari Jumpponen

Ecosystem effects of biodiversity manipulations in European grasslands.

We present a multisite analysis of the relationship between plant diversity and ecosystem functioning within the European BIODEPTH network of plant-diversity manipulation experiments. We report results of the analysis of 11 variables addressing several aspects of key ecosystem processes like biomass production, resource use (space, light, and nitrogen), and decomposition, measured across three years in plots of varying plant species richness at eight different European grassland field sites. Differences among sites explained substantial and significant amounts of the variation of most of the ecosystem processes examined. However, against this background of geographic variation, all the aspects of plant diversity and composition we examined (i.e., both numbers and types of species and functional groups) produced significant, mostly positive impacts on ecosystem processes. Analyses using the additive partitioning method revealed that complementarity effects (greater net yields than predicted from monocultures due to resource partitioning, positive interactions, etc.) were stronger and more consistent than selection effects (the covariance between monoculture yield and change in yield in mixtures) caused by dominance of species with particular traits. In general, communities with a higher diversity of species and functional groups were more productive and utilized resources more completely by intercepting more light, taking up more nitrogen, and occupying more of the available space. Diversity had significant effects through both increased vegetation cover and greater nitrogen retention by plants when this resource was more abundant through N2 fixation by legumes. However, additional positive diversity effects remained even after controlling for differences in vegetation cover and for the presence of legumes in communities. Diversity effects were stronger on above- than belowground processes. In particular, clear diversity effects on decomposition were only observed at one of the eight sites. The ecosystem effects of plant diversity also varied between sites and years. In general, diversity effects were lowest in the first year and stronger later in the experiment, indicating that they were not transitional due to community establishment. These analyses of our complete ecosystem process data set largely reinforce our previous results, and those from comparable biodiversity experiments, and extend the generality of diversity–ecosystem functioning relationships to multiple sites, years, and processes.

Dark septate endophytes - are they mycorrhizal?

Abstract. Dark septate endophytes (DSE) are a miscellaneous group of ascomycetous anamorphic fungi that colonize root tissues intracellularly and intercellularly. The limited selection of studies quoted here exemplifies the range of host responses to symbiotic DSE fungi. Like mycorrhizal associations, DSE associations vary from negative to neutral and positive when measured by host performance or host tissue nutrient concentrations. This range of host responses is partially attributable to variation between different fungus taxa and strains. Similarly, hosts differ in their responses to a single DSE strain. Experimental conditions may also govern the nature of the symbiotic association. It is concluded that DSE are capable of forming mutualistic associations functionally similar to mycorrhizas. If the variation in host response to mycorrhizal fungi is considered to represent a continuum ranging from parasitism to mutualism, DSE symbiosis must be considered mycorrhizal, at least under some conditions.

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere.

* This study targeted the fungal communities in the phyllosphere of Quercus macrocarpa and compared the fungal species richness, diversity and community composition among trees located within and outside a small urban center using recently developed 454 sequencing and DNA tagging. * The results indicate that the fungal phyllosphere communities are extremely diverse and strongly dominated by ascomycetes, with Microsphaeropsis [two Operational Taxonomic Units (OTUs); 23.6%], Alternaria (six OTUs; 16.1%), Epicoccum (one OTU; 6.0%) and Erysiphe (two OTUs; 5.9%) as the most abundant genera. * Although the sequencing effort averaged 1000 reads per tree and detected nearly 700 distinct molecular OTUs at 95% internal transcribed spacer 1 similarity, the richness of the hyperdiverse phyllosphere communities could not be reliably estimated as nearly one-half of the molecular OTUs were singletons. * The fungal communities within and outside the urban center differed in richness and diversity, which were lower within the urban development. The two land-use types contained communities that were distinct and more than 10% of the molecular OTUs differed in their frequency.

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Summary 1. The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and BLAST searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. 2. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. 3. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. 4. ITSx paves the way for more sensitive BLAST searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.

Ecosystem properties and microbial community changes in primary succession on a glacier forefront

Abstract We studied microbial community composition in a primary successional chronosequence on the forefront of Lyman Glacier, Washington, United States. We sampled microbial communities in soil from nonvegetated areas and under the canopies of mycorrhizal and nonmycorrhizal plants from 20- to 80-year-old zones along the successional gradient. Three independent measures of microbial biomass were used: substrate-induced respiration (SIR), phospholipid fatty acid (PLFA) analysis, and direct microscopic counts. All methods indicated that biomass increased over successional time in the nonvegetated soil. PLFA analysis indicated that the microbial biomass was greater under the plant canopies than in the nonvegetated soils; the microbial community composition was clearly different between these two types of soils. Over the successional gradient, the microbial community shifted from bacterial-dominated to fungal-dominated. Microbial respiration increased while specific activity (respiration per unit biomass) decreased in nonvegetated soils over the successional gradient. We proposed and evaluated new parameters for estimating the C use efficiency of the soil microbial community: “Max” indicates the maximal respiration rate and “Acc” the total C released from the sample after a standard amount of substrate is added. These, as well as the corresponding specific activities (calculated as Max and Acc per unit biomass), decreased sharply over the successional gradient. Our study suggests that during the early stages of succession the microbial community cannot incorporate all the added substrate into its biomass, but rapidly increases its respiration. The later-stage microbial community cannot reach as high a rate of respiration per unit biomass but remains in an “energy-saving state,” accumulating C to its biomass.

Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites.

We analysed two sites within and outside an urban development in a rural background to estimate the fungal richness, diversity and community composition in Quercus spp. ectomycorrhizas using massively parallel 454‐sequencing in combination with DNA‐tagging. Our analyses indicated that shallow sequencing (∼150 sequences) of a large number of samples (192 in total) provided data that allowed identification of seasonal trends within the fungal communities: putative root‐associated antagonists and saprobes that were abundant early in the growing season were replaced by common ectomycorrhizal fungi in the course of the growing season. Ordination analyses identified a number of factors that were correlated with the observed communities including host species as well as soil organic matter, nutrient and heavy metal enrichment. Overall, our application of the high throughput 454 sequencing provided an expedient means for characterization of fungal communities.

Species abundance distributions and richness estimations in fungal metagenomics – lessons learned from community ecology

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log‐normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant‐associated fungal communities – phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log‐normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log‐normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data – a log‐normal model for the core group and a log‐series model for the satellite group. The prominent log‐series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.

How plant diversity and legumes affect nitrogen dynamics in experimental grassland communities

Abstract. Positive relationships between species richness and ecosystem processes such as productivity or nitrogen cycling can be the result of a number of mechanisms. We examined how species richness, biomass, and legume presence, diversity, and abundance explained nitrogen dynamics in experimental grassland plots in northern Sweden. Nitrogen concentrations and δ15N values were measured in plants grown in 28 mixtures (58 plots) including 1, 2, 4, 8 or 12 local grassland species over four years. Values for δ15N declined over time for all three functional groups (grasses, legumes, and non-leguminous forbs), suggesting greater reliance on N fixed by legumes over time by all species. Above ground percent nitrogen (%N) also declined over time but root %N and total N did not. Path analysis of above ground data suggested that two main factors affected %N and the size of the N pool. First, higher plant diversity (species richness) increased total N through increased biomass in the plot. Although in the first two years of the experiment this was the result of a greater probability of inclusion of at least one legume, in the last two years diversity had a significant effect on biomass beyond this effect. Second, percent legumes planted in the plots had a strong effect on above ground %N and δ15N, but a much smaller effect on above ground biomass. In contrast, greater plant diversity affected N in roots both by increasing biomass and by decreasing %N (after controlling for effects mediated by root biomass and legume biomass). Increased legume biomass resulted in higher %N and lower δ15N for both non-legume forbs and grasses in the first year, but only for grasses in the third year. We conclude that a sampling effect (greater probability of including a legume) contributed towards greater biomass and total N in high-diversity communities early on in the experiment, but that over time this effect weakened and other positive effects of diversity became more important.

Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments

*The fungal richness, diversity and community composition in the Quercus macrocarpa phyllosphere were compared across a growing season in trees located in six stands within and outside a small urban center using 454-sequencing and DNA tagging. The approaches did not differentiate between endophytic and epiphytic fungal communities. *Fungi accumulated in the phyllosphere rapidly and communities were temporally dynamic, with more than a third of the analyzed operational taxonomic units (OTUs) and half of the BLAST-inferred genera showing distinct seasonal patterns. The seasonal patterns could be explained by fungal life cycles or environmental tolerances. *The communities were hyperdiverse and differed between the urban and nonurban stands, albeit not consistently across the growing season. Foliar macronutrients (nitrogen (N), potassium (K) and sulfur (S)), micronutrients (boron (B), manganese (Mn) and selenium (Se)) and trace elements (cadmium (Cd), lead (Pb) and zinc (Zn)) were enriched in the urban trees, probably as a result of anthropogenic activities. Because of correlations with the experimental layout, these chemical elements should not be considered as community drivers without further empirical studies. *We suggest that a combination of mechanisms leads to differences between urban and nonurban communities. Among those are stand isolation and size, nutrient and pollutant accumulation plus stand management, including fertilization and litter removal.

Utilization of major detrital substrates by dark-septate, root endophytes'

Utilization of major forms of carbon, nitrogen and phosphorus commonly present in plant litter and detritus was determined for cultures of Phialophora finlandia, Phialocephala fortinii and five dar...